GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Phyllobacterium endophyticum PEPV15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_106719566.1 CU100_RS26145 amidase

Query= curated2:A1ATL3
         (485 letters)



>NCBI__GCF_003010935.1:WP_106719566.1
          Length = 488

 Score =  199 bits (505), Expect = 2e-55
 Identities = 150/489 (30%), Positives = 227/489 (46%), Gaps = 38/489 (7%)

Query: 2   DLFDLTLHELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADR- 60
           DL  L +  L     + ++S+ E T A L RIA+ + ++NA++ V  + A   A + D  
Sbjct: 10  DLCFLPVSRLSEMRATGKISTAEITEAYLSRIAKFDSKLNAYVEVYAKEARLAATSLDAG 69

Query: 61  RIAAGEADVLTGIPLAVKDIFLTEGTLTTCGSRILNNFIPPYSATSFEKLKQRGMVLLGK 120
           R    +  +  GIP+A+KD+   +G +TT GS          +A+   +L   G ++LGK
Sbjct: 70  RDTRNDGGLACGIPIALKDLLEVDGKITTAGSAHFRGRRSCVTASLARRLISSGSIILGK 129

Query: 121 LNQDEFAMGSSNESSASGPCRNPWNTDC--IPGGSSGGSAAAIAARQATVTLGTDTGGSI 178
               EFA      +   G   NPW+ D   IPGGSS GSA A++   A   +GTDTGGS+
Sbjct: 130 TQTVEFAYSGWGINPQMGTPWNPWDEDIQRIPGGSSSGSAVAVSGSLAPWAIGTDTGGSV 189

Query: 179 RQPASHCGCVGLKPTYGRVSRYGVIAYASSLDQVGPLTRDVTDCAIMLGALAGHDPKDST 238
           R PAS CG   LK T  +++  G+I  + + D  GP+TR V D AI+   + G + + + 
Sbjct: 190 RLPASFCGVTALKTTADQIATDGIIPLSKTFDTPGPITRSVLDAAILYNVMLGSESQFAF 249

Query: 239 SVDRPVPDYQAALTNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLGAEFTEISL 298
                V     AL   + GL++G   +   EG++ DV  + D+++ET   LGAE  E +L
Sbjct: 250 G-SGTVIGISRALEGGVLGLKLGSLPKAEREGVEADVLEAYDRSLETLSNLGAEIVETNL 308

Query: 299 P-HTDYAVASYYLIATAEASANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGSEVKRR 357
           P         +  I  +EA A         F    +    LL+             V+  
Sbjct: 309 PFRFQDCFGPHMSIVNSEAYA--------YFRDVIDDGSSLLD-----------ESVREG 349

Query: 358 IMLGTYALSSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIG--EKVN 415
           I  G       Y DA+     +  +   A    A   VD +LTP   + A  +   ++  
Sbjct: 350 ISAGRTISPQQYSDAF-----EQISRFKAQISGALVNVDALLTPTTLSVALPVEGLDRSR 404

Query: 416 DPLQMYLSDIFTIPVNLAGTCAMSLPAGISGQGLPIGVQLIGKPFGEETILRAAHAFEQA 475
            P +      FT  VN  G C ++LP G + + LP  +Q++ +   E   LR   AF+QA
Sbjct: 405 PPSR------FTRFVNTLGMCGLALPNGKNAEDLPTSLQIVCREHQERLALRIGLAFQQA 458

Query: 476 TEWHSLRAP 484
           T WH LR P
Sbjct: 459 TSWH-LRRP 466


Lambda     K      H
   0.318    0.134    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 496
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 485
Length of database: 488
Length adjustment: 34
Effective length of query: 451
Effective length of database: 454
Effective search space:   204754
Effective search space used:   204754
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory